This is pretty common with me when I play games with lots of colors, moving/dynamic objects, and an upbeat tone in general. Like when I play those Super Crazy Guitar Maniac flash games, even when I look away my sight is still scrolling like the screen. Sometimes happens with launcher games as well (Toss the Turtle, Learn to Fly, Flight, Hedgehog Launch, etc.). I believe it has to do with the visuals making you dizzy from their distracting rapid visuals. So what I recommend for games like these is to obviously take breaks often, more so than ones with calmer visuals. However, if it really is just to do with the flashing objects, that's beyond my help as it may be something to do with epilepsy, and I don't know anyone with it so I'm going to refrain with trying to sound smart and helpful there. That's more of the medical-condition tier than the distracting-visuals-making-me-dizzy tier, heh.

TL;DR: Take breaks more often than usual for games with distracting visuals if you think it's eye strain, if something more serious ask someone more professional.